Publications related to GHI - Gestion

Diverse cell-specific patterns of alternative polyadenylation in Drosophila

Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids. We trace dynamic 3' UTR patterns across cell lineages, including in the male germline, and discover new APA patterns in the intestinal stem cell lineage. Finally, we correlate expression of RNA binding proteins (RBPs), miRNAs and global levels of cleavage and polyadenylation (CPA) factors in several cell types that exhibit characteristic APA landscapes, yielding candidate regulators of transcriptome complexity. These analyses provide a comprehensive foundation for future investigations of mechanisms and biological impacts of alternative 3' isoforms across the major cell types of this widely-studied model organism.

NATURE PORTFOLIO2022

Recent advances in trajectory inference from single-cell omics data

Bart Deplancke, Wouter Saelens

Trajectory inference methods have emerged as a novel class of single-cell bioinformatics tools to study cellular dynamics at unprecedented resolution. Initial development focused on adapting methods based on clustering or graph traversal, but recent advances extend the field in different directions. A first class of methods includes novel probabilistic methods that report uncertainties about their outputs, and new methods that consider complementary knowledge, such as unspliced mRNA, time point information, or other types of omics data to construct the trajectory. A second class of methods uses the obtained trajectories as a starting point for novel analyses, such as visualization approaches, new types of statistical analyses, and the possibility to render static analyses more dynamic, such as dynamic gene regulatory network inference.

ELSEVIER2021

MarrowQuant 2.0: clinical application of a user-friendly digital hematopathology tool for human bone marrow trephine biopsies

Bart Deplancke, Olaia Maria Naveiras Torres-Quiroga, Rita Sarkis

SPRINGER2022

Live-seq enables temporal transcriptomic recording of single cells

Wanze Chen, Riccardo Dainese, Bart Deplancke, Vincent Roland Julien Gardeux, Pernille Yde Rainer, Wouter Saelens, Magda Zachara

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy(2,3), thus allowing to couple a cell's ground-state transcriptome to its downstream molecular or phenotypic behaviour. To benchmark Live-seq, we used cell growth, functional responses and whole-cell transcriptome read-outs to demonstrate that Live-seq can accurately stratify diverse cell types and states without inducing major cellular perturbations. As a proof of concept, we show that Live-seq can be used to directly map a cell's trajectory by sequentially profiling the transcriptomes of individual macrophages before and after lipopolysaccharide (LPS) stimulation, and of adipose stromal cells pre- and post-differentiation. In addition, we demonstrate that Live-seq can function as a transcriptomic recorder by preregistering the transcriptomes of individual macrophages that were subsequently monitored by time-lapse imaging after LPS exposure. This enabled the unsupervised, genome-wide ranking of genes on the basis of their ability to affect macrophage LPS response heterogeneity, revealing basal Nfkbia expression level and cell cycle state as important phenotypic determinants, which we experimentally validated. Thus, Live-seq can address a broad range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

NATURE PORTFOLIO2022

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner

Daniel Alpern, Bart Deplancke, Radiana Ferrero, Horia Hashimi, Maria Litovchenko, Pernille Yde Rainer, Julie Marie Russeil, Magda Zachara

Adipose stem and precursor cells (ASPCs) give rise to adipocytes and determine the composition and plasticity of adipose tissue. Recently, several studies have demonstrated that ASPCs partition into at least three distinct cell subpopulations, including the enigmatic CD142(+) cells. An outstanding challenge is to functionally characterise this population, as discrepant properties, from adipogenic to non- and anti-adipogenic, have been reported for these cells. To resolve these phenotypic ambiguities, we characterised mammalian subcutaneous CD142(+) ASPCs across various experimental conditions, demonstrating that CD142(+) ASPCs exhibit high molecular and phenotypic robustness. Specifically, we find these cells to be firmly non- and anti-adipogenic both in vitro and in vivo, with their inhibitory signals also impacting adipogenic human cells. However, these CD142(+) ASPC-specific properties exhibit surprising temporal phenotypic alterations, and emerge only in an age-dependent manner. Finally, using multi-omic and functional assays, we show that the inhibitory nature of these adipogenesis-regulatory CD142(+) ASPCs (Aregs) is driven by specifically expressed secretory factors that cooperate with the retinoic acid signalling pathway to transform the adipogenic state of CD142(-) ASPCs into a non-adipogenic, Areg-like state.

WILEY2022

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Multidrug therapy (MDT) has been successfully used in the treatment of leprosy. However, although patients are cured after the completion of MDT, leprosy reactions, permanent disability, and occasional relapse/reinfection are frequently observed in patients. The immune system of multibacillary patients (MB) is not able to mount an effective cellular immune response against M. leprae. Consequently, clearance of bacilli from the body is a slow process and after 12 doses of MDT not all MB patients reduce bacillary index (BI). In this context, we recruited MB patients at the uptake and after 12-month of MDT. Patients were stratified according to the level of reduction of the BI after 12 doses MDT. A reduction of at least one log in BI was necessary to be considered a responder patient. We evaluated the pattern of host gene expression in skin samples with RNA sequencing before and after MDT and between samples from patients with or without one log reduction in BI. Our results demonstrated that after 12 doses of MDT there was a reduction in genes associated with lipid metabolism, inflammatory response, and cellular immune response among responders (APOBEC3A, LGALS17A, CXCL13, CXCL9, CALHM6, and IFNG). Also, by comparing MB patients with lower BI reduction versus responder patients, we identified high expression of CDH19, TMPRSS4, PAX3, FA2H, HLA-V, FABP7, and SERPINA11 before MDT. From the most differentially expressed genes, we observed that MDT modulates pathways related to immune response and lipid metabolism in skin cells from MB patients after MDT, with higher expression of genes like CYP11A1, that are associated with cholesterol metabolism in the group with the worst response to treatment. Altogether, the data presented contribute to elucidate gene signatures and identify differentially expressed genes associated with MDT outcomes in MB patients.

FRONTIERS MEDIA SA2022

A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle

Benjamin D. Cosgrove, Maria Deak, Bart Deplancke, Sonia Karaz, Umji Lee, Julie Marie Russeil

Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and meta-bolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator of the Apln promoter. Single-cell analysis of regenerating muscle revealed that the apelin receptor (Aplnr) is enriched in endothelial cells, whereas Tead1 is enriched in myogenic cells. Knock-down of Tead1 stimulates Apln secretion from muscle cells in vitro and myofiber-specific overexpression of Tead1 suppresses Apln secretion in vivo. Apln secretion via Tead1 knock-down in muscle cells stimulates endothelial cell expansion via endothelial Aplnr. In vivo, Apln peptide supplementation enhances endothelial cell expansion while Tead1 muscle overexpression delays endothelial remodeling following muscle injury. Our work describes a novel paracrine crosstalk in which Apln secretion is controlled by Tead1 in myogenic cells and influences endothelial remodeling during muscle repair.

CELL PRESS2022

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Daniel Alpern, Riccardo Dainese, Mustafa Demir, Bart Deplancke

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said method.

2022

Single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae

Melanie Blokesch, Natalia Carolina Drebes Dörr, Milena Jadwiga Jaskolska, Alexis Joseph Proutière, Sandrine Stutzmann

Vibrio cholerae is a well-studied human pathogen that is also a common inhabitant of marine habitats. In both environments, the bacterium is subject to interbacterial competition. A molecular nanomachine that is often involved in such competitive behavior is the type VI secretion system (T6SS). Interestingly and in contrast to non-pandemic or environmental isolates, the T6SS of the O1 El Tor clade of V. cholerae, which is responsible for the ongoing 7th cholera pandemic, is largely silent under standard laboratory culture conditions. Instead, these strains induce their full T6SS capacity only under specific conditions such as growth on chitinous surfaces (signaled through TfoX and QstR) or when the cells encounter low intracellular c-di-GMP levels (TfoY-driven). In this study, we identified a single nucleotide polymorphism (SNP) within an intergenic region of the major T6SS gene cluster of V. cholerae that determines the T6SS status of the cell. We show that SNP conversion is sufficient to induce T6SS production in numerous pandemic strains, while the converse approach renders non-pandemic/environmental V. cholerae strains T6SS-silent. We further demonstrate that SNP-dependent T6SS production occurs independently of the known T6SS regulators TfoX, QstR, and TfoY. Finally, we identify a putative promoter region adjacent to the identified SNP that is required for all forms of T6SS regulation in V. cholerae.

2022

Solving the mystery of the missing plasmids in seventh pandemic Vibrio cholerae strains

Melanie Blokesch

The pathogen responsible for the continuing seventh cholera pandemic typically lacks self-replicating plasmids. Genetics, cell biology and bioinformatics analyses have identified two DNA-defence systems that protect bacterial populations from plasmids and bacteriophages, and that might have shaped the evolution of modern Vibrio cholerae.

2022